Head teachers' union, ASCL, said the move was wholly unacceptable and is threatening legal action.
The headteachers' union ASCL said quality of learning was more important than hours spent in the classroom.
Head teachers represented by the Association of School and College Leaders (ASCL) back the ending of the January exams.
Head teachers are likely to challenge Mr Gove on the issue when he addresses the ASCL conference later on Friday.
Brian Lightman, leader of the Association of School and College Leaders (ASCL), emphasised the lack of enthusiasm for localised pay negotiations.
Brian Lightman, general secretary of the Association of School and College Leaders (ASCL), said the statistics should encourage people to "ask more probing questions".
Brian Lightman, general secretary of the ASCL head teachers' union, described the move to a voluntary qualification as detrimental to raising the status of heads.
The Association of School and College Leaders (ASCL) said the proposals would not improve social mobility and would have a "damaging effect" on pupils from the most deprived areas.
"A-levels are a well known and well respected international brand and it would be foolish to damage confidence in them for no compelling reason, " said ASCL leader Brian Lightman.
Brian Lightman, of the Association of School and College Leaders (ASCL), whose annual conference opens on Friday, suggested that some schools might decide simply to do three A-levels and ignore AS-levels altogether.
Head teachers have told ASCL this can take up to two hours, whereas in the past many schools would have been able to raise the alarm about a pupil over the telephone.
Speaking to the BBC after his meeting with the watchdog, Brian Lightman, general secretary of ASCL, said the issue was not re-marking papers, but altering grade boundaries and "putting right what's happened".
The Association of School and College Leaders (ASCL) said the decision flew in the face of overwhelming feedback from a recent consultation that found that the "current system needs tweaking but is broadly fit for purpose".
According to Dr John Dunford, of the Association of School and College Leaders (ASCL), one factor driving the increase in pupils studying the sciences separately, is that schools seeking to specialise in science need to offer subjects in this way.
"Now that we have looked at all the evidence and made final preparations for the court case, we remain certain that it is the right thing to do, " said Brian Lightman of the Association of School and College Leaders (ASCL).
An ASCL survey suggested that more than 80% of heads of further education colleges, sixth form colleges and schools with sixth forms believed they would have to reduce the choice of courses they offered while 83% said they believed this age group should attract more rather than less funding than younger pupils.
BBC: Sixth-form funding dip 'could stymie' talent, Gove warned
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